The polkit support has mostly been implemented on an “as needed” basis. At present, it has mostly been based on what gnome-software needed, which so far hasn’t included snap configuration.
With that said, it would be hard to provide a comprehensible message to go with the generic
snap set command, so the user is aware of what access they’re granting.
With the current infrastructure, the easiest way to provide a custom polkit action ID (and message) would be to add a new API for changing the refresh policy. This wouldn’t imply changing how the policy is stored: just adding an extra way to change it.